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Extensive functional overlap between σ factors in Escherichia coli

Nature Structural & Molecular Biology volume 13, pages 806–814 (2006)Cite this article

Abstract

Bacterial core RNA polymerase (RNAP) must associate with a σ factor to recognize promoter sequences. Escherichia coli encodes seven σ factors, each believed to be specific for a largely distinct subset of promoters. Using microarrays representing the entire E. coli genome, we identify 87 in vivo targets of σ32, the heat-shock σ factor, and estimate that there are 120–150 σ32 promoters in total. Unexpectedly, 25% of these σ32 targets are located within coding regions, suggesting novel regulatory roles for σ32. The majority of σ32 promoter targets overlap with those of σ70, the housekeeping σ factor. Furthermore, their DNA sequence motifs are often interdigitated, with RNAPσ70 and RNAPσ32 initiating transcription in vitro with similar efficiency and from identical positions. σE-regulated promoters also overlap extensively with those for σ70. These results suggest that extensive functional overlap between σ factors is an important phenomenon.

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Figure 1: In vivo binding of σ32 and RNAP to previously identified σ32 target promoters.
Figure 2: In vivo binding of σ32 and RNAP to novel σ32 targets not located in known promoter regions.
Figure 3: Extensive overlap between σ70 targets and targets of σ32 and σE.
Figure 4: Transcription from heat-shock promoters by Eσ70 and Eσ32 in vitro.

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Acknowledgements

We thank G. Butland, J. Greenblatt and A. Emili (University of Toronto) for the TAP-tagged rpoH strain, N. Reppas, R.J. Geisberg, Z. Moqtaderi, M. Schwabish, X. Fan and L.T. Westblade for helpful discussions and C. Baisden for expert technical assistance. We also thank C. Gross for communicating results before publication. J.T.W. was supported by a Charles A. King Trust Postdoctoral Fellowship, Bank of America, Co-Trustee. This work was supported by US National Institutes of Health grants GM30186 (K.S.), and GM72814 and GM58750 (E.N.).

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Authors and Affiliations

  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, 02115, Massachusetts, USA

    Joseph T Wade & Kevin Struhl

  2. Department of Biochemistry, New York University School of Medicine, New York, 10016, New York, USA

    Daniel Castro Roa & Evgeny Nudler

  3. School of Biosciences, The University of Birmingham, Edgbaston, B15 2TT, Birmingham, UK

    David C Grainger & Stephen J W Busby

  4. Oxford Gene Technology, Begbroke Science Park, Sandy Lane, Yarnton, OX5 1PF, Oxford, UK

    Douglas Hurd

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Correspondence to Kevin Struhl or Evgeny Nudler.

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Supplementary information

Supplementary Fig. 1

Purified σ factors. (PDF 183 kb)

Supplementary Fig. 2

Formation of the promoter-proximal elongation complex (EC18) by Eσ70 and Eσ32 at the groE template. (PDF 87 kb)

Supplementary Fig. 3

Overlap between σE targets and targets of σ70. (PDF 99 kb)

Supplementary Fig. 4

Transcription from σE promoters by Eσ70 in vitro. (PDF 147 kb)

Supplementary Table 1

Summary of genome coordinates used in analyses. (XLS 142 kb)

Supplementary Data

Transcript map and genome-wide binding data for σ70. (PDF 88 kb)

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Wade, J., Roa, D., Grainger, D. et al. Extensive functional overlap between σ factors in Escherichia coli. Nat Struct Mol Biol 13, 806–814 (2006). https://doi.org/10.1038/nsmb1130

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